Legend:

required parameter

advanced parameter

+FeatureFinderMetaboAssembles metabolite features from singleton mass traces.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FeatureFinderMetabo'

in input centroided mzML fileinput file*.mzML

out output featureXML file with metabolite featuresoutput file*.featureXML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAlgorithm parameters section

++++common

noise_threshold_int10 Intensity threshold below which peaks are regarded as noise.

chrom_peak_snr3 Minimum signal-to-noise a mass trace should have.

chrom_fwhm5 Expected chromatographic peak width (in seconds).

++++mtd

mass_error_ppm20 Allowed mass deviation (in ppm).

reestimate_mt_sdtrue Enables dynamic re-estimation of m/z variance during mass trace collection stage.true,false

min_sample_rate0.5 Minimum fraction of scans along the mass trace that must contain a peak.

min_trace_length5 Minimum expected length of a mass trace (in seconds).

++++epd

width_filteringoff Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.off,fixed,auto

min_fwhm3 Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto.

max_fwhm60 Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto.

masstrace_snr_filteringfalse Apply post-filtering by signal-to-noise ratio after smoothing.false,true

min_trace_length5 Minimum length of a mass trace (in seconds).

max_trace_length300 Maximum length of a mass trace (in seconds).

++++ffm

local_rt_range10 RT range where to look for coeluting mass traces

local_mz_range6.5 MZ range where to look for isotopic mass traces

charge_lower_bound1 Lowest charge state to consider

charge_upper_bound3 Highest charge state to consider

report_summed_intsfalse Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.false,true

disable_isotope_filteringfalse Disable isotope filtering.false,true

isotope_modelmetabolites Change type of isotope model.metabolites,peptides

use_smoothed_intensitiestrue Use LOWESS intensities instead of raw intensities.false,true